

package net.seqalign.test;

import net.seqalign.*;
import net.matvec.*;
import net.prot.*;

import java.util.*;

public class SeqMutate {

    public static void main(String[] args){
	Align a = new Align();
	if (!a.parseArgs(args)){
	    System.out.println("Error parsing args.");
	    System.exit(1);
	}
	if (!a.loadAlgoData()){
	    System.out.println("Error loading algo data.");
	    System.exit(1);
	}

	List<StringBuilder> seqs = new ArrayList<StringBuilder>();
	for (String s : Align.sequences){
	    seqs.add(new StringBuilder(s));
	}

	System.out.println("Sequences:");
	for (String str : Align.sequences){
	    System.out.println(" >" + str);
	}
	AlignmentSolution s = new AlignmentSolution(seqs);
	System.out.println("Mutated sequences:");
	for (StringBuilder seq : seqs){
	    s.mutate(seq, Align.temp);
	    System.out.println(" >" + seq);
	}
    }

}
